: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Thursday, 5 March 2009 11:10 AM
To: Prapti Gautam
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec error in analyze
Prapti,
Try deleting the directory 'qdec/Untitled' and run it again. Prior to
v4.2.0, qdec did not delete
Julia,
If you haven't already tried this, can you make sure that your display
is set to use 'millions' of colors (thats the Mac OS's way of setting
24bit color).
If that doesnt matter, you can try using the newest freesurfer, v4.1.0,
which is built against vtk v5.2, which is newer than what is
Hi,
I’ve run across the following error while trying to run qdec in my linux 64 bit
computer,
qdec.bin: error while loading shared libraries: libtiff.so.3: cannot open
shared object file: No such file or directory
Is there any specific file that I need to download or change configuration
Hi Prapti,
I think you have to modify the $LD_LIBRARY_PATH shell variable.
first find where libtiff.so.3 is. Usually locate libtiff.so.3 will tell
you
where the file is at. On my machine, it is in /usr/lib/ and /usr/lib64/
then
LD_LIBRARY_PATH = $LD_LIBRARY_PATH:/usr/lib64/
export LD_LIBRARY_PATH
It's possible that you are running a Debian-based distro and just
don't have libtiff.so.3; but you probably have libtiff.so.4, so you
can create a symlink so that libtiff.so.3 points to libtiff.so.4.
I have to do this In Debian etch and later
mjp
On Nov 26, 2008, at 4:26 PM, Siddharth
Hi,
Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command prompt.
While the splash screen did appear with the inflated brain surface, the qdec
interface did not appear (even after 10min). When I tried to CTRL-C the
terminal window, the following error message appeared:
[EMAIL
Jenifer,
Is this new to v405, or have prior versions also had this problem?
Are you running directly from the terminal? Or over an ssh or vnc
connection? If over vnc, from what kind of machine?
Nick
On Wed, 2008-07-23 at 11:14 -0500, Juranek, Jenifer wrote:
Hi,
Running Freesurfer v405 on
-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Wed 7/23/2008 3:47 PM
To: Juranek, Jenifer
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
Jenifer,
Is this new to v405, or have prior versions also had this problem?
Are you running directly
for any help you can provide,
Jenifer
-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Wed 7/23/2008 3:47 PM
To: Juranek, Jenifer
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
Jenifer,
Is this new
: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Wed 7/23/2008 4:04 PM
To: Juranek, Jenifer
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
Jenifer,
In the file /etc/X11/xorg.conf, within the section titled Section
Module, make sure this line exists
Hi, I am getting a qdec error on FreeSurfer 4.0.2 on Tiger. The error has
been mentioned on the forum before. In particular qdec.bin seems to be
calling for tcl/tk libs in /usr/pubsw which doesn't exist. Below are the
first two lines from the ldd profile for qdec.bin.
ldd
Ming,
I'm planning on releasing a new freesurfer v4.0.5 this week, which will
include a distribution for Tiger on Intel.
Nick
On Tue, 2008-06-10 at 02:39 -0500, Ming Hsu wrote:
Hi, I am getting a qdec error on FreeSurfer 4.0.2 on Tiger. The error has
been mentioned on the forum before. In
Hello,
In February William McGarry has reported a qdec error (see original
message from William below) and to fix this error a new version of
fsgdfPlot.tcl was sent to him. We have not found any comment from
William whether this file has actually solved his problem but we have
the very same
-
Hi
FOrgot to attach the file of lh.cortex.label with my last email. Here it is.
My error message is the same as Sky's: see
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07271.html
Looked like there was no solution for it at the time (April 17th, 2008),
what about now
-
Thanks Doug.
Do I need to rerun everything or at least rerun the average step? I went
straight into qdec but the same error message appears (after replacing
the old mri-mergelabels with the one just downloaded.
Wei Wen
Doug Greve wrote:
This may be a problem with the way that the unix
I think you can just run make_cortex_label for your average subject.
Wen, Wei wrote:
-
Thanks Doug.
Do I need to rerun everything or at least rerun the average step? I
went straight into qdec but the same error message appears (after
replacing the old mri-mergelabels with the one just
-
Hi Doug,
I ran make_cortex_label (that went through) for my average subject which
was mas_average and tried qdec again but still the same message:
mri_glmfit: could not parse 149955th line in
/home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label
ERROR reading
-
Hi Doug,
Perhaps it was this: after make_cortex_label instead of replacing the
original lh.cortex.label with this newly generated one, it creates
lh.cortex2.label. I renamed this lh.cortex2.label into
lh.cortex.label and so far so good.
Perhaps we need to regenerate the average anyway in
You might have to delete the old cortex.label
Wen, Wei wrote:
-
Hi Doug,
I ran make_cortex_label (that went through) for my average subject
which was mas_average and tried qdec again but still the same message:
mri_glmfit: could not parse 149955th line in
Yes, if it finds it there, it will create the 2 instead of
overwriting. You should not have to regenerate the average, but that
should work now too.
Wen, Wei wrote:
-
Hi Doug,
Perhaps it was this: after make_cortex_label instead of replacing
the original lh.cortex.label with this newly
Hi Bruce,
Here are the first few lines of the lh.cortex.label:
#label , from subject ??
149955
==
/cind/00/FSv4Test/Freesurfer/subjects/average/make_cortex_label.tmp.20230/lh.G_and_S_occipital_inferior.label
==
161841 -37.845 -74.578 -13.988 0.00
161842 -37.786 -74.111 -14.300 0.00
that looks okay. What about the last two lines?
On Thu, 17 Apr 2008, Sky
Raptentsetsang wrote:
Hi Bruce,
Here are the first few lines of the lh.cortex.label:
#label , from subject ??
149955
==/cind/00/FSv4Test/Freesurfer/subjects/average/make_cortex_label.tmp.20230/lh.G_a
Hello Freesurfers,
I am having troubles analyzing some data in the qdec tool. I have two
groups of the same subjects that were run with different versions of FS
and I have put them in the same SUBJECTS_DIR and smoothed and created an
average subject. I have made a qdec.table.dat file and the
Hi Sky,
what are the first few lines of:
/cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
is your partition full?
Bruce
On Wed,
16 Apr 2008, Sky Raptentsetsang
wrote:
Hello Freesurfers,
I am having troubles analyzing some data in the qdec tool. I have two
groups of
Sky,
Can you load the lh.cortex.label file in tksurfer? If not, then its
corrupted somehow, and would need to be recreated outside of qdec.
Nick
On Wed, 2008-04-16 at 17:49 -0700, Sky Raptentsetsang wrote:
Hello Freesurfers,
I am having troubles analyzing some data in the qdec tool. I have
Mischka,
You mention that you created your own average subject (this is fine,
although the default 'fsaverage' subject is sufficient in most cases, as
the average is used just for display). If you do choose to create and
use your own average subject, two things to keep in mind are:
- include
Thanks Nick, (sorry I did't response this mail before in the proper way)
I copied your file and the IsWindowShowing error was fixed, but the second
error persists:
ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWApplication.cxx,
line 1182
vtkKWQdecApp (0x87903e0): TclTk error:
Dear FS-Experts,
I am trying to run Freesurfer on a Ubuntu 7.10 (Gutsy Gibbon) system and
unfortunately I encounter the same problem that Gonzalo Sanchez
Benavides and also William McGarry described in earlier emails. Copying
the new fsgdfPlot.tcl into the $FREESURFER_HOME/lib/tcl directory
Hi all,
I'm trying to run qdec on a SL 4.5:
[EMAIL PROTECTED] ~]$ uname -a
Linux neuro01.pic.es 2.6.9-55.0.12.ELsmp #1 SMP Thu Nov 1 08:41:34 CST 2007
i686 i686 i386 GNU/Linux
[EMAIL PROTECTED] ~]$ /lib/libc.so.6
GNU C Library stable release version 2.3.4, by Roland McGrath et al.
Copyright (C)
Gonzalo,
Attached is a file called fsgdfPlot.tcl, which was missing from
freesurfer v4.0.2. Copy it to your $FREESURFER_HOME/lib/tcl directory.
Nick
On Wed, 2008-03-05 at 12:42 +0100, Gonzalo Sanchez Benavides wrote:
Hi all,
I'm trying to run qdec on a SL 4.5:
[EMAIL PROTECTED] ~]$
Hi,
I pasted an error that I am receiving in qdec below. SUBJECTS_DIR is
/space/lightning/2/users/NEAA-freesurfer. If you need any more information
from me I will be happy to provide it. Any help is much appreciated.
Thanks,
troy:cameo[87] ERROR: QdecGlmDesign::GenerateContrasts: factor 1
Woo-Suk,
A file was missing from the distribution. That file, fsgdfPlot.tcl, is
attached to this email. Copy it to:
$FREESURFER_HOME/lib/tcl
Nick
On Mon, 2008-02-11 at 11:03 +0900, Woo-Suk, Tae wrote:
I've processed my data with FreeSurfer 3.04,
and ran the group data with qdec of
Ryan,
It appears that tcsh is not being used. Enter tcsh by typing:
tcsh
then initialize freesurfer by typing:
source $FREESURFER_HOME/SetUpFreeSurfer.csh
then try the qdec utility again (and if still gives the same problems,
then run the ldd command and send me the results).
You can
[EMAIL PROTECTED] qdec]$ source FREESURFER_HOME/bin/tcl_setup
bash: /usr/local/freesurfer/bin/tcl_setup: line 48: syntax error near
unexpected token `setenv'
bash: /usr/local/freesurfer/bin/tcl_setup: line 48: `if ( -e
$TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3'
[EMAIL
[EMAIL PROTECTED] ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
freesurfer-Linux-rh9-stable-pub-v4.0.2
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
Ryan,
Can you send me the output of:
ldd $FREESURFER_HOME/bin/qdec.bin
This error, and one seen by George He, who also is using Fedora release
8, tells me that the problem is related to Tcl/Tk on that platform.
Freesurfer includes a Tcl/Tk/Tix/BLT bundle in its distribution, so I
dont know why
Ryan,
I forgot to mention, prior to running the ldd command, type this:
source $FREESURFER_HOME/bin/tcl_setup
source $FREESURFER_HOME/bin/vtk_setup
source $FREESURFER_HOME/bin/kww_setup
Also, it should not be necessary to download a tcl/tk package, as the
tcl/tk package included with freesurfer
When trying to analyze some data in qdec, after I completed recon-all -all and
-qcache for the subjects in my qdec table, I get to the Display tab and pick an
option under Scalar. It doesn't matter which option, as they all give me the
same two errors repeatedly (forcing me to quit qdec). These
I downloaded some packages for tcl and tk, but they didn't have any effect. I
also get this error, which I forgot to include:
ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx,
line 221
vtkKWQdecApp (0x881c1f0): Script:
FsgdfPlot_IsWindowShowing 0
Returned Error on
Mike,
This qdec error results from a slightly out-of-date tcl script (an
oversight on my part when I updated qdec for v4.0.2). Attached to this
email is the file fsgdfPlot.tcl, which contains the function
FsdgfPlot_IsWindowShowing, and should be copied to
$FREESURFER_HOME/lib/tcl (overwriting
Hello,
First, ... Happy New Year!
When trying to run a basic qdec analysis between two groups (using qdec
from FS v4.0.2), I get an error in a pop-up window, which I've screen-
captured and attached as a gif. This is a Linux-centos4 installation,
and it doesn't have a /usr/pubsw directory, so
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